The Associate Online and Community Specialist of Capcom U.S.A, Yuri L. Araujo stated the below about Monster Hunter 3 Ultimate:

As for the online support, we’ve announced the Wii U can go online. 3DS has local multiplayer only. If that’s something you really want to see happen, head on to the MH forums and start talking about it there – then I can bring it up the chain with some supporting evidence. =)

Araujo brings out that only the Wii U version of Monster Hunter 3 Ultimate will feature online play while the 3DS will just feature local multiplayer. He does bring out hope though that maybe the 3DS version will feature online if enough people want it.