Loose......unless they're MIB, lol!
I have most ponies loose (all my G1s and G2s are loose) because they take up less space, but, more importantly, because I like to have access to them unfettered by a box!
However, there are certain ponies in the G3s and G4s that for (mainly arbitrary reasons!) are MIB/MIP. All my Winter Series G3s are MIB and all my G4 Snowglobe ponies are MIB...just the way the cookie crumbled...
It's entirely up to you! You could always have one of each if you're in two minds (I did this with Sunset Shimmer...one MOC, one loose!) then you can have the best of both worlds. Might need to choose carefully though if funds are not unlimited (which, sadly, mine are not!)