Hi there,
What time will you arrive at Narita Airport? I don't think it will be a problem to travel to Matsumoto. You can always come to the station early and queue on the platform for a non reserved seat but I think you should be fine if you reserve the seats on day of arrival.
Also you can use this website to reserve seats for JR East in advance:
http://www.eki-net.com/pc/jreast-shinkansen-reservation/English/wb/JRTicket/SeatReservation/RouteSearch.aspx
This includes travel from Shinjuku to Matsumoto. The best route to take is the Narita Express to Shinjuku, Tokyo and the Azusa express train from there to Matsumoto. Some rules and regulations apply for the above website, so be sure to read them carefully. You also have to collect the tickets the day beforehand before 9 pm.
Hope this helps,
Daniel