The sizes are relative. Just because the 29er has bigger wheels it is not necessarily a "bigger" bike so the sizes will be comparable. My 26" bike is a L and my 29er is a 21" frame which would be a L or XL.
29er sizes tend to run a little different in a lot of brands. If you have a bike you like, measure or look up the effective top tube length. That should give you an approximate size for 29ers to try. Don't be afraid to try bigger and smaller too, though.
"Don't buy upgrades; ride up grades." -Eddy Merckx