It's tricky when space is limited. There aren't many good small stereo speakers. Kanto YU2 and Audioengine A2+ are two examples. Steljes NS1, were an exception, but they are no longer available.
If those smaller speakers would still be too big, then I think you'll have to go with 2.1, as stereo speakers that small, it really restricts what frequencies the speaker can output; hence why many 2.1 speakers have small satellite speakers with the subwoofer.
2.1 speakers might not be too bad a choice though, given that they'll be used only for gaming. The one thing that most 2.1 speakers really suck at, is when used for music. Considering they won't be used for music, that won't matter. Plus the additional bass provided by a subwoofer, might be welcome, given that is the one area that lacks the smaller a speaker gets.
Logitech Z623 get decent comments.