I have had this problem many times before as immigration lines can be very unpredictable. The ground staff will know you are connecting from an international flight, and as such, if you don't show up, they will assume that you are probably stuck in immigration. EWR handles many international flights, so they should be very used to this type of misconnect and they will rebook your friend for free. Generally, they are very flexible about these types of misconnects.
As you mentioned, the next flight is 9:30PM, and hopefully you are out of immigration by then. Once you miss the original flight, they will rebook you on the next flight. If you miss the 9:30PM, they will then rebook you on the first flight the next day. I've never had this happen before (even when I was stuck in immigration for over 4 hours one time, there was still a flight the same day), so I do not know if they will provide a hotel. If they don't, it would probably be cheaper for your friend to just take one of the many cheap buses that goes from NYC to Boston.
Even if you have checked baggage it is not an issue. Ordinarily, you have to pick up your baggage after immigration to bring it through customs, then give the baggage back to the airline for the domestic portion. If you are stuck in immigration and it is getting close to your flight, the airline will actually take your baggage and clear customs for you (i.e. have customs open and check your bag and clear it). That way they can bring your bag through to the domestic flight so that it may be ready in case you clear immigration in time for your flight. They won't load the bag unless you make the flight, and if you don't, they will simply put the bag onto whatever flight you actually end up on.