Yes, withdrawals from an IRA are taxable income. If you had withholding, that goes on your account as a credit, but your income and taxes are calculated just one time a year on your tax return. If you had too much withheld, you get a refund of the excess. But income is income.
Having other taxable income can make your social security benefit partly taxable. And taking more money from your IRA in one year compared to another year increases your income and might affect your eligibility for credit and other benefits.
I can't tell you exactly how your income would affect your spouse's PTC, but the whole PTC system was designed badly in the first place.
