Oh Boy! A first time visitor! Fresh meat for all the urban myths and legends!
But seriously, most of the advice above has been well-founded. If you're a Marriott kind of guy, by all means stay at the Marquis. It's one of their flagship properties now, it's relatively new, and you won't be disappointed. Besides, you may as well be in the middle of the new Times Square eating shopping and looking "mall". If only they could bring back about 25% of the old sleaze, but no more. I know, it doesn't work that way. I blame the Mayor and PremEx, in that order.
Do yourself a favor and banish all thoughts of a car from your mind. (The same advice applies to downtown Chicago, Washington, and New Orleans.) We don't want you filling your neighbors in on the secret of the discount $35 per day parking garages you found. Honestly, driving is not the way we New Yorkers show our best face to the world, even if the biggest offenders are from New Jersey and Pakistan.
One more thing: stop in Chicago on the way and bring some warm weather with you.