If the bonds are held through Treasury Direct then the Treasury will issue the Form 1099 INT. Otherwise they come from the bank that redeemed them. For example, the Treasury Direct web page on Series EE/E savings bonds explains that:
You can see the interest on your IRS Form 1099-INT.
- If a financial institution pays the bond, you will receive a paper 1099-INT from that financial institution either soon after you redeem your bonds or within the first two months after the end of the year in which you redeem your bonds.
- If you redeem electronic bonds in your TreasuryDirect account, your 1099-INT will be available through your account.
So the issuer of the Form 1099-INT for savings bonds depends on how they are held and redeemed. It might be the Treasury or it might be a bank.