I was born with congenital heart issues, is it safe to take thyroid medication (levothyroxine t4)? i read the side effects affect the heart?

Missing information. The majority of congenital heart issues that do not require surgical repair have no significant impact on later life, but the issues with each can differ. I doubt simple thyroid replacement meds would have any negative effect on a stable person. It is prescribed to replace a hormone the body would otherwise make, so it balances the system. You don't take an excess in any case.

Yes. Too much or too little can cause heart disease related to thyroid hormone.