What is the best way to file if I'm self-employed, married, but my spouse's income is not taxable (Disability)?

Typically, it is better to file using the Married Filing Jointly filing status as any credits would not be limited.  

Please see the link below for more information.

Is it better to file jointly or separately?

Does she get Social Security Disability SSDI?  It might be partly taxable.  You have to enter the SSA-1099 into your return.  If you file separately she would have to file a return and report it and it would become taxable.

Up to 85% of Social Security becomes taxable when all your other income plus 1/2 your social security, reaches:

Married Filing Jointly: $32,000

Single or head of household: $25,000

Married Filing Separately: 0