I'm not an accountant, so this isn't accounting advice. For that, please consult with an accountant. However . . .
If both you and your husband otherwise qualify, yes. Here's what the IRS says:
S6. I have been estranged from my spouse for over three years and file married filing separate. I donâ€™t know if my spouse has owned a main home in the last three years, but I have not. If I buy a house in 2009 that otherwise qualifies for the first-time homebuyer credit, can I claim the credit?
A. Section 36(c)(1) requires that the taxpayer and the taxpayer's spouse not have an ownership interest in a principal residence within the three years prior to the date of purchase. While individuals do not have to be married to get the credit, marriage (and legal separation) imputes ownership of a previous home upon the other spouse. If your spouse has not owned a main home in the last three years, then you may claim the credit.
That's at http://www.irs.gov/newsroom/article/0,,id=206294,00.html
Be sure to verify that with your accountant.