Jurisdiction works on the defendant, not the plaintiff/prosecution (or rather, it's waived for them since they chose to initiate the action).
So yes, if the NSA and CIA already have proof that Lavabit serves some minimum amount of customers in those states then it would be proper to bring it in that federal district.
But it seems like they a) wouldn't have the proof needed until they got access to lavabit's assets or b) if they had the proof, they wouldn't need formal access to lavabit's assets
Kind of a circular problem but of course since we don't know what he's appealing and why...
Edit: Actually they could just use credit card information to establish customers so nvm
Edit2: Now that I've read a copy of the search warrant linked by someone else in this thread, I see what's going on
