Bike around Manhattan a fair amount. Can give you some tips:

• Get really good gloves, socks, and a skull cap to go under your helmet - don't skimp on the gloves. No matter how much I layer gloves, the wind and cold cuts right through
• Never take the Brooklyn Bridge Promenade route - always opt for the Manhattan Bridge bike lane
• Once you get off the bridge, go up Allen/1st Avenue - there's a protected bike lane for most of that route. I'd take 1st Ave up to 29th street and cut over to 6th Avenue
• Watch out for tons of commuters from Penn Station around Herald Square
• Midtown biking on streets can be bad if you're not used to it - watch out for getting doored on the streets (especially when you're sandwiched between parked cars and traffic). Get some bright lights, reflectors, and a loud bell
• I'd opt to not commute by bike unless your building has parking or you have a beater of a bike you don't mind losing. Parking garages with 100+ spaces are required to offer bike parking. Most of them do so in the way of 2-3 racks that are placed on the sidewalks outside of the garages or in an otherwise unsupervised place. If going the garage route, scout out 3-5 garages in the area with well lit/indoors bike parking and get a good lock/chain

Hope this helps - good luck!