Hi,

I am a resident alien and my spouse is a non-resident alien. We were married in 2007. My spouse has been in the US for 4 years on an F1 visa (hence she is a non-resident alien) and she has her own SSN. If we file as married filing jointly using form 1040 for the federal income tax return, will we qualify for the economic stimulus rebate check? Thank you for helping out.

Yes, you can file joint return as residents and will get recovery rebate.
Your spouse must start paying FICA taxes on her income. Read Your U.S. Tax Return: Filing Status for Married

Actually, payment of FICA taxes will not start for your wife until after her FIFTH year on F-1 status, or when she converts to an H-1 or H-1B visa.