If chinese ships would behave nicely and sit peacfully in harbours, then yes, a massive tomahawk strike could wipe out a good deal of PLAN's inventory. But thinking bout it realistically, that will never be the case. Or are you suggesting that US would strike first, before china even makes a move and tries to invade taiwan? I don't believe that'd happen. So, what i'm talking about is a scenario where china is already on the move. Where a good deal of ships are out in the sea, where good deal of airplanes are in the air, etc. China can do training runs, not make anything out of those wargames for 100 times, then 101st time attack for real. War in kosovo wasn't many years ago, it was just 6 years ago. And block 3 tomahawks were used, just like in iraq two years ago. Yes, in this potential new war, block 4s would be used, but the difference between those two is slim compared to difference between serbian air denfenses and EW systems and those of china's. Actually, let's be concrete, and talk about two scenarios, one - worst case for US, where china attacks now when USN has under a thousand tomahawks, mostly block 3s, the same kind used in serbia - and scenario two, happening around 2010 - where US has replenished its inventory and has around 3000 mostly block 4 tomahawks. By then chinese forces will be stronger and more modern, too.
As for chinese air force, you can only slow down its progress in a taiwan invasion scenario by hitting the airbases with tomahawks. Without real air power, US can not prevent the invasion with tomahawks alone.
You did mention sub surface combatants... i assume you mean subs other than tomahawk carrying ones, too. Yes, that'd help greatly but it wouldn't guarantee anything and it'd come at great cost. Without air support and so close to china, those subs would be dead the moment they're detected. And they would be detected, simply because of the relatively small area around taiwan and large force china has at its disposal. In the open sea us nuclear subs would have a great edge over chinese SSKs but close to shore, in the shallows, where SSKs would be protecting and not attacking - that edge would all but disappear.
So, to sum it up, yes, US is perfectly capable of ruining any potential china's plans to occupy taiwan but it'd need a full war machine to do it. Just subs and especially just cruise missiles wouldn't cut it, in my opinion.