Here are my recommendations:

1. book a Fairmont room using the NFAF rate (which can be combined with the certs )
2. send the General Manager an e-mail that this is a special occasion, you´d like to use your certs and ask him what he can arrange (make sure to mention you stay there very often)

Officially the best deal would be using a free night cert or a 3rd night free cert (doesn´t make a difference if you´re staying 3 nights) and a suite upgrade which would give you the best available suite (excl. specialty suite)
EDIT: The "standard" suites at the Fairmont Chicago IMO look very nice (700 sq ft, seperate sitting area and dining area), so getting one of those wouldn´t be a bad deal at all.

Considering your frequent stays you could play dumb and politely ask if you´d combine a room upgrade cert and a suite upgrade cert to get a Gold room or a specialty suite, if they´ve any availability.

You should be able to achieve your goal for <$250 (excl. food etc.).

Good luck!

P.S. If you have any dining certs left over, don´t forget to use these for dining or the spa.