Is masturbation worse than smoking (for the Catholic Church)?

The very first requirement for something to be a mortal sin is what is called "grave matter":

For a sin to be mortal, three conditions must together be met: "Mortal sin is sin whose object is grave matter and which is also committed with full knowledge and deliberate consent."

(Catechism of the Catholic Church paragraph 1857; the quote is from the apostolic exhortation Reconciliatio et paenitentia of Pope St. John Paul II)

The very next paragraph defines "grave matter": "Grave matter is specified by the Ten Commandments". In other words, in order for a sin to be mortal, it must be (among other things) a violation of one or more of the Ten Commandments.

The Church considers masturbation to be a violation of the sixth commandment:

You shall not commit adultery. [Exodus 20:14]

You have heard that it was said, "You shall not commit adultery." But I say to you that every one who looks at a woman lustfully has already committed adultery with her in his heart. [Matt. 5:27–28]

(Catechism of the Catholic Church, before paragraph 2331)

The Magisterium of the Church - in the course of a constant tradition - and the moral sense of the faithful have declared without hesitation that masturbation is an intrinsically and seriously disordered act. ...

A person therefore sins mortally not only when his action comes from direct contempt for love of God and neighbor, but also when he consciously and freely, for whatever reason, chooses something which is seriously disordered. For in this choice, as has been said above, there is already included contempt for the Divine commandment: the person turns himself away from God and loses charity. Now according to Christian tradition and the Church's teaching, and as right reason also recognizes, the moral order of sexuality involves such high values of human life that every direct violation of this order is objectively serious.

(Persona Humana, Declaration on Certain Questions Concerning Sexual Ethics, Declaration of the Congregation for the Doctrine of the Faith; section 9, emphasis added)

For this reason, masturbation is always grave matter. (Whether it is a mortal sin in any given circumstance depends on the other requirements for mortal sin, a matter for pastoral judgment.)

Smoking, on the other hand, does not typically seem to be a direct violation of any commandment. You do refer to smoking in the Catechism, paragraphs 2290 and 2291. Here they are:

The virtue of temperance disposes us to avoid every kind of excess: the abuse of food, alcohol, tobacco, or medicine. Those incur grave guilt who, by drunkenness or a love of speed, endanger their own and others' safety on the road, at sea, or in the air.

The use of drugs inflicts very grave damage on human health and life. Their use, except on strictly therapeutic grounds, is a grave offense. Clandestine production of and trafficking in drugs are scandalous practices. They constitute direct co-operation in evil, since they encourage people to practices gravely contrary to the moral law.

These paragraphs are part of a broader discussion of respect for one's own health, which in turn falls in a discussion of the fifth commandment:

You shall not kill. [Exodus 20:13]

You have heard that it was said to the men of old, "You shall not kill: and whoever kills shall be liable to judgment." But I say to you that every one who is angry with his brother shall be liable to judgment. [Matt. 5:21–22]

(Catechism of the Catholic Church, before paragraph 2258)

It thus appears that smoking in excess may be a mortal sin. On the other hand, by the time one smokes "in excess", one may already be addicted to nicotine; and addiction, insofar as it reduces a person's ability to act with "deliberate consent", may reduce the severity of the wrong, even to the point that it is no longer a mortal sin.

Thus, if the Church were to say (and it has not, to the best of my knowledge) that "Masturbation is worse than smoking", what it would mean by that is "Masturbation is a more serious sin than smoking, generally speaking; more likely than smoking to 'destroy charity in the heart of man' and 'turn man away from God, who is his ultimate end and his beatitude'" (Catechism paragraph 1855). It is in that sense—the only one relevant to the Church—that masturbation can be "worse" than smoking.

Note: Since I wrote this answer, it appears, you've edited your question to add a number of arguments to support your thesis that smoking is more harmful than masturbation. Let's go through those:

• As others have noted, your point (1) states (whether you mean it to or not) that given any two harmful activities, one "natural" and one "artificial", the "artificial" one is necessarily worse. This is not so; your "therefore" part doesn't follow from your "because" part. You need to either provide more support for your "therefore" ("smoking is ... more harmful") or else rephrase your point.
• Points 2–5 and 9 appear to address the physical perils of smoking as compared with those of masturbation. There are two points to be made here:
  • The physical dangers of smoking develop not with smoking itself, but with repetition of smoking. That is, it is not the inhaling of a single puff, one time, that produces these ill effects, but repeating that activity many times a day, over the course of days, weeks, months, or longer. The mere activity of smoking is not necessarily in itself harmful.
  • Although certainly the Church will pay attention to the possible physical ill effects of an activity in deciding how morally serious it is, it's not those ill effects which make something immoral, but rather the effect of the activity on one's relationship with God.
• Points 6 and 7 appear to be arguing that masturbation is less harmful because it is regarded in society as less harmful. This is a fallacy again. Two hundred years ago, smoking was considered less harmful than masturbation—but its physical and moral effects were doubtless the same. One can't conclude that something is (relatively) harmless simply because society considers it so.
• Finally, point 8 implies that those who are addicted to drugs are more dangerous to society than those who mast**bate. Even if this can be extended to those who smoke (it's a stretch at best), again it's true that the morality of a behavior doesn't depend on the risk a person poses to society because of it.

The Church's approach simply says this:

• It's possible to smoke without significantly harming one's health. Someone may be able to take for example one puff, from one cigarette, once in their life, without harming themselves.
• On the other hand, choosing to mast**bate requires one to think in a certain way about sex. How one thinks about sex is intimately tied to how one thinks about the love between two humans; and this love in turn (as Catholics believe) is designed to reflect the love of God for people and vice versa. Thus it's simply not possible in Catholic understanding to mast**bate—even once—without revealing that one has at best a severely distorted view of what God's love is like, which leads to an inability to receive God's love as it truly is. It's this inability which makes the deliberate choice to mast**bate always a mortal sin in the Church's eyes.