Best route to take into NYC...?

Driving in to Manhattan at 9 AM will be a nightmare.

A far better option would be to drive to near Manhattan, say, the Jersey side, park the car at a facility there, and then take transit into Manhattan. If you have a hotel booking in Manhattan, go look at what the charge for parking will be, it will be a big one.

An alternate route is to come in from the North, thus avoiding the NYC Hudson crossings. Take the 17/I-86 to Route 6 (The switch occurs where 17 meets the I-87), and cross the Hudson on the Bear Mountain Bridge. Continue east on the 6 to the Taconic State Parkway south, stick with it when it turns into the Sprain Brook, then shift over to the I-87 via Rt 100, and then enter Manhattan on the Third Avenue Bridge, which takes you from Exit 3 in The Bronx to Manhattan.

Take 17 to 87 (Tappan Zee Bridge) and then down 9A. 9A is clear all the way other than when you merge in with the GWB traffic but by 9 that's usually not bad -- typically will cost you an extra 20 minutes.

Anything coming through Jersey seems like a much bigger risk.

There is absolutely NO GOOD WAY to get into Manhattan at 9-ish on a weekday. Of your mentioned alternatives, the GW seems like the better bet because there's no reason to go further south than you have to in order to wind up in the same situation as you would on the George.

There are other ways to approach the city, but they're all equally bad at that hour of the day.