We have taken Silver b/t SJU and EIS at least a half dozen times in the last 4-5 years, also as a JetBlue code share. Only one time were we significantly delayed. All of the other times we were slightly delayed, but not enough to cause stress with respect to a connection.

When booking these flights, we always allow for extra time in SJU in case the outbound Silver flight is late.

Considering your other options into EIS (taking aside the fact that many prefer the ferry), Silver is about as good as any. Having taken the MIA-EIS route, this is preferred most of all.