Do I claim income from box 3 on 1099-MISC? It was income to cover expenses for townhome (taken form tenant's deposit)?

Yes, forfeited security deposit is income. Since the deposit was used to cover repairs, the repairs are a deduction, if the deposit is income. Enter this on Schedule E as rent.

Please see this answer from Howard 1948.

From IRS Topic 414 re Rental Income:

Security deposits – Do not include a security deposit in your income if you may be required to return it to the tenant at the end of the lease. If you keep part or all of the security deposit because the tenant breaks the lease by vacating the property early, include the amount you keep in your income in that year. If you keep part or all of the security deposit because the tenant damaged the property and you must make repairs, include the amount you keep in that year if your practice is to deduct the cost of repairs as expenses. To the extent the security deposit reimburses those expenses, do not include the amount in income if your practice is not to deduct the cost of repairs as expenses. If a security deposit amount is to be used as the tenant's final month's rent, it is advance rent that you include as income when you receive it, rather than when you apply it to the last month's rent.