It is only September! Ok well tomorrow it is October! This is very very early. If your son is applying to some civilian schools as well you already probably know unless there is rolling admissions he won't get an acceptance this soon.
From what I recall in other years - USNA seems to issue most of their LOA's in October. A lot can happen in a few weeks.
Okay - you son feels though he has a dilemma - he has an LOA to USMA but not to USNA. What to do about nominations?
The decision to nominate a candidate rests with each individual member of congress. There is nothing that NY says that keeps your US Representative from awarding him two nominations. Yes, many MOC's do "talk" but the decision rests with each office.
Your son is going to have to choose eventually. He should be honest on the application and pick the academy which is his first choice.
If Navy is his first choice then he should pick it.
Make absolutely sure he applies for the Vice Presidential nomination.
If he has an LOA from USMA and he doesn't get a nomination from his MOC - talk to admissions. More than likely they will "find" him one. It may be the VP nom (which is chosen by each academy) or a Superintendent's nomination. He also may not receive his appointment until later in the spring. Bottom line is - West Point wants your son. If he makes a good faith effort to gain a nominations then admissions will take care of him.
If your son is confused about what to do then he should call the nominations manager in the congressman's and senator's office. They usually are very helpful.
If your son has questions about the status of his USNA application then he should call the Navy admissions office.
I suggest you read through this thread, it illustrates the importance of candidates like your son applying for the VP nomination:
http://www.serviceacademyforums.com/showthread.php?t=2131