I came to US in July 2005 with F1 visa. Now I am on OPT. I filed 1040NR form for federal tax. I can't apply ITIN for my wife because I believe I am a non-resident alien and a non-resident alient can't file jointly.
Now I want to file jointly for state tax because I can be treated as a resident in MA. My question is: how can I get a ITIN for my wife if we can't file jointly for federal tax?

Double check your facts. The states typically require you file the state return the same way you file the federal return, which would be Married Filing Separately in your case.