I guess the best thing you can do is make a contingency plan. Run it by the good folks here.
She may come back and say nothing. Play it by ear.
If she comes back and wants a separation/divorce, don't fight her on it. You can pull the "I don't want to make hasty decisions" speech only for so long and the mysterious, "I have a lot to think about" line for a limited amount of time. If she's resolute in wanting a divorce, you dragging your heels will only give away your power and get you hit by the divorce truck she's driving.
You are strong, you have a sense of self, and you have things YOU want.
You reminding her you DON'T want a divorce while you are divorcing is kind of weak and pathetic. If she sees your serious about moving on without her, she might take notice.
If you were to divorce, what do YOU want?
Shared custody?
Her to move out?
Sell the house, etc?
If she wants to move to NYC -- she's free to go. You and the kids stay in your home in Boston. She can come up every other weekend and hang with them.
Most of us who had cheating spouses acted like we were footnotes in our spouses life. It's YOUR life. You need to act like you are the main character in your own play.
As an aside there's a lot of research on lost loves (It's called the Lost Love Project). Affairs that re-kindle a past romance are VERY powerful and are almost irresistible. They succeed at about the same rate as regular affairs (5% of the time). If she does leave you and marries him, that marriage has only a 25% chance of succeeding. This means it will, most likely, burn out. However. she will put you through hell before it's done. You may not have the emotional resolve to outlast her affair. She sees younger self in her ex boyfriend. This [censored]. Of course, you don't have to sit around and wait for her to get tired of her lover. You have options.