It also depends on which VS flight you are travelling on. If its the early morning VS45 then you may make your connection but it will be close. However if its a later flight then be prepared for conjestion in immigration. Several international flights arrive in JFK T1 around the time the VS3 and VS9 arrive and it can take upwards of an hour just to get through.
You will have to collect your baggage and re check it, minimising bag size to a carry on will save you time. Also with the higher level of security in the US it could take a while to get to the departure lounge once you reach T9.
I don't mean to spread doom and gloom but if possible it may be better to re schedule your San Juan departure to allow more time.
I have tried walking to other terminals in JFK - its better to take the bus.
Hope this helps