First, I would really REALLY try to take the full three months. First babies are a big adjustment, and especially if you plan on breast feeding, I think you'll really want that time. After three months there's a good chance you won't be fully physically recovered (not sore or anything, but just not feeling like yourself, still quite a bit of extra weight, etc.) but even moreso, you'll likely still be quite sleep deprived. That (other than leaving the baby) is probably the toughest part about going back to work.
You may be able to take leave without pay. That seems to vary a lot within the government by agency. I'm not sure if you can afford that, but my guess is that LWOP is your only option, since the government has limited options in terms of what they can offer employees. You could also maybe work out a teleworking arrangement for a few months, but I wouldn't give up my three months for that. Teleworking still means working; it just saves you the commute and time getting yourself ready.
I know that Fed pay is often pretty formulaic, but you might also see if you can get an increase in salary or a signing bonus if you have to take LWOP. I did that in the private sector, but again, I know working for the Feds is different. That said, when I was a Fed, the salary options were sometimes flexible, although sometimes they weren't.