The only way to ensure that you get to pick your seat is by calling direct. Purchasing realtime tickets is available for most broadway shows - online stores usually require that you call in to secure your seat and pay for the tickets over the phone. Purchase Tix - has great selection of online seating - they also have the ability to purchase online direct. There are are a variety of different selects for each budget range.
Jersey Boys Tickets for New York range from 112 to 420 in the orchestra.