Still looking for it on Tomato, but if it's anything like DD-WRT, there should be the option to block it under the Access Restrictions section. The
Tomato Wiki does have a section that refers to that so give it a try.
DD-WRT even has the protocols listed under msnmessenger and msn-filetransfer.
The only thing to watch out for is that using these restrictions can slow down the router as they use packet inspection (DD-WRT does anyway) as I found out recently after the 10 meg upgrade.
Edit: Here you go - about half way down someone covers how to do exactly what you're after.