I agree that unless your inbound flight is delayed, you should make it. I'm, not sure what DL's minimum connection time is, but they do take into account the time to clear customs. If 90 minutes were below the threshhold, they wouldn't have let you book it.

I see flights at 4:20p, 6:40p, 9:00p most days. If you don't see one of those, it may be sold out on your day of travel, but that does not mean that if you misconnect, that you might not be able to get on it anyway. Even sold out flights sometimes accomodate standbys (due to no-shows), and misconnecting passengers are usually at the top of the list.

In any case, there doesn't seem to be much to do about it now. Your connection time is what it is. So plan ahead, but try not to stress too much.

US hotels will keep your hotel reservations past midnight, assuming you held it with a credit card. Still, if you do find yourself rebooked such that you won't arrive until that late, it's not a bad idea to call the hotel while you're waiting around JFK and let them know that you will be arriving very late.

Edit to add: if running that late, call the rental car company too.