It can indeed be tough -
First let me say he's a lucky guy in that it's hard for you to be apart and encouraging - that's probably why you are also great friends as well as BF/GF. The kind of silly/stupid answer to this question, all be it a valid one:
Q: What do I say to encourage him/help him through these seemingly endless low spots/points while he is - homesick, pissed off, questioning his decision, missing everything that used to be great and normal about his life now he finds himself waking up early to eat a meal he didn't even used to know existed (breakfast) so he can go clean toilets other people use before going to classes while all his friends are still on the beach ...? (Did I miss any of the usual p/c complaints/kvetches this time of year, if so please add them...)
A: dumb but straight answer: Anything that usually works from a) nothing except the verbal and or facebook chat equivalent between yourselves that is equivalent to a sympathetic/supportive nod to z) anything that helps him forget his current issues and think about either the reasons he made the decision (hopes/dreams/goals) or the next intermediate milestone when things will change a little and signal to him that he's on a journey toward a goal and is getting closer to it...even if it's really 4 years away.
Seriously, you're a great person/friend to ask this and my little bit of humor here isn't to poke fun at anybody - you as a member of his support network have to see a little humor in all this to keep your sanity too, if you're going to continue to be the supportive person he vents to or else you might loose it (your positive attitude) too.
As mentioned I tend to try and get folks to "chunk" the year into eight parts - just go and look at my other posts on this subject on this thread: Low Morale):
http://www.serviceacademyforums.com/showthread.php?t=14138
and you can see that if you and he do that then there's going to be some sort of intermediate milestone each of the next 6-7 weeks. If this year at the USMMA is similar to others, your BF will also see that during each of these phases the focus of his day to day existence changes and generally gets a little more "normal" while at the same time his outlook and approach to things also change as he acclimates to life at USMMA... In the end all this should make it easier for him and make him less prone to want to throw in the towel - even though he being human will still have trying times...
This is one of the toughest times for P/Cs so what he's going through isn't unique - that's both good and bad since that means he's likely to have a few friends in his company who are also at low points and they can either help each other to get out of their current "funk" or drive each other further into it. The best way for them to help each other out of it is to stay active and do things together vice sitting in the barracks lamenting their lots in life. Whether that's going to O'Hara and lifting weights, playing basketball or beating each other's brains out on the racquetball courts, or going down to the waterfront and sailing every day they can, etc. Anything can be better than just sitting in the barracks as a P/C and usually is....
Of course he may not be looking for any advice at all from you - he may only be looking for a shoulder to cry on and missing both his GF and best friend and just wanting to hear you still miss him. Seriously, don't forget to to tell him that because from time to time one of his friends in the barracks is likely to receive a "Dear John" letter and that will no doubt trigger some fears and concerns on his part - even if he doesn't express them directly to you...
Hope this helps and I can honestly say that after seeing your post I am rooting for both he and you.