I can choose either of the above routes, 3.5 hour layover in JFK or 1 hr 50 min layover in AMS. I would rather go through AMS as I like the times better but I am concerned whether the connection time is too short. Any advice appreciated. Both choices are on Delta.

I'll be more comfortable with a 1:50 connection at AMS than a 5-hour one at JFK.

Delays on the BOS-JFK route are very common, especially if the weather is windy and/or rainy. You'd have a very low probability of missing the connection via AMS, and that low probability would likely be worsened, not improved, by traveling via JFK. I can't think of a single reason to go via JFK (other than schedule times, if that's essentia).

Thanks to you both for clear concise helpful answers!

I agree with both of those people. Plus, it is SO nice to go through customs at Logan rather than at JFK.

One caveat - they are very thorough at Amsterdam security so don't dawdle on the way to your gate.

We actually have changed plans and are going BOS-ZRH-BCN returning BIO-MUC-BOS. Thanks for help, though!