Welcome to the Big Apple! I have a few recommendation for you to:
Groomer
I highly recommend Pat Smith at the Ritzy Canine Carriage House
(Armani has been going to her since she was a baby)
Doggy Daycare/Dog Sitting
Ritzy Canine Carriage House
Pet Grooming New York Dog Grooming Nyc Dog Boarding New York Cat Grooming Pet Boarding dog groomer Pet Sitting nyc Ritzy Canine Carriage House
(They have a nice boutique for shopping on premise as well)
Vet/24 Hour Care
Park East Animal Hospital
http://www.parkeastanimalhospital.com
(Armani has been going there since her first well puppy visit when she first came home)
Boutique
You will find really nice stuff at Trixie and Peanut
Designer dog clothes, designer dog collars, designer dog beds, designer dog carriers | Trixie + Peanut Bargain Outlet
I just discovered Unleahed By Petco (It is new, clean, nice products, friendly staff)
Unleashed by PETCO - Home Page
Your babies will be fine on the subway in a bag - we do it all the time.
Have a sweet summer in NY!