Frecciarossa
 

My flight from JFK to MXP is due to arrive at 10:40. I want to make reservations for the Frecciarossa to Rome. What would be the earliest time I should plan on?

You need to take the Malpensa Express to Milano Centrale first.
The 12:13 seems feasible, arriving Milano Cle at 13:05. Should you miss it, the next one is 30 minutes later so arriving Milano at 13:35.

So I would opt for the 2pm non-stop service (arriving Roma Termini at 5:40) as it allows a possible mishap.

Regarding FrecciaRossa, there are 3 fares (super economy, economy, base).
To get some flexibility, but an economy fare. You may change your ticket for an earlier / later train by paying the difference to the full fare (at a ticket office or a machine).