I found several older posts of similar issues and they were advised to split their 1099-INT forms. In my case that would be one 1099 form in Turbotax with my Box 1 interest, and a separate one for the same institution with my box 3 interest along with the accrued interest that goes along with it.
I think that may be a better idea than just subtracting the accrued interest from the interest myself, as it will keep the accrued interest line on my schedule B along with interest amounts that can be matched to the various boxes on the 1099s.
These are the other links I saw:
https://ttlc.intuit.com/community/state-taxes/discussion/interest-income-exempt-in-nj/00/2230450
https://ttlc.intuit.com/community/taxes/discussion/accrued-interest-paid-when-purchase-bonds-is-not-...
https://ttlc.intuit.com/community/investments-and-rental-properties/discussion/tax-exempt-bonds-more...
