There are actually a lot of Chicago boutique hotels and like many hotels they provide spa services to their guests too.

Hotel Burnham in Chicago is one of the best boutique hotels in Chicago. They also have in-room spa services that you can indulge in. You can get massage treatments, body and facial treatments at a good price. You can even buy some of their spa products so you could experience that same spa treatment at home.

http://www.burnhamhotel.com/chicago-hotel-services/in-room-spa.html

Dana Hotel and Spa is a boutique hotel that is, well, also a spa. It's no longer the traditional Dana hotel that it was before. It's now a modern hotel with all the luxury that you can handle. They have the most comprehensive spa treatments in a hotel.

http://www.danahotelandspa.com/spa/treatments/index.cfm

There are many other boutique hotels in Chicago that you could choose from. It depends on your taste and budget but there's really one for every tourist and businessmen out there. Just check out this great link to find the list of boutique hotels in Chicago.

http://www.hotelrooms.com/Boutique_Hotels_USA_Chicago.htm