I have installed crysis mods, I purchased crysis on steam. Just look up how to install the mods for that particular game. All the folders are the same, there just in the steam folder on the c drive somewhere.
From my own experience, almost all mods/games can be modded even if the game was purchased from Steam. I know Crysis, Oblivion, and the Witcher all work via Steam, and I'm not currently aware of anything that specifically *doesn't* work with Steam. So, on the whole, it's a pretty safe bet it should work.
The one caveat to be aware of with mods and Steam is version dependencies since Steam handles the version updates for you. If the Steam version does not match the version that the mod requires you might be SOL. I've run into this with CIV4 mods where the Steam version is newer than what some older mods require and you can't roll back like a non-Steam game. Although less likely it's possible that Steam may not have the most recent updates and mods might not work for that reason.