Well, rather than Hotels, boutique or otherwise, you might try renting an apartment. I've used http://www.airbnb.com when we stayed in Paris for 10 days and it's an excellent service with wide ranging choice ... and it's very cost effective. about 7 years ago
I completely agree, you should try to stay with airbnb (http://fr.airbnb.com/?af=523075&c=direct_link) somewhere in the area called "Vieux Lille" or near "Gare Lille Flandres".
Try to find somewhere you can park, as Lille is not easy to park a car. almost 6 years ago