I sold stock on 12/30 to take my RMD, but it did not clear until January 3rd. I believe I have to file a 5329 to report it to the IRS, but I can't find the form.

The procedure depends on if you have a 1099-R to complete, and if you are using TurboTax Online or Desktop.

If you have a 1099-R for another distribution, and you are using TurboTax Online or Desktop:

1. Enter the information from the form (s) and proceed through the interview until you reach a screen : Did You Miss a Required Distribution From Any Retirement Accounts? 
2. You then continue to enter the account name, and the amount of RMD due by 12/31.
3. Continue through the interview, and select whether or not you wish to fill out a waiver statement to request that the penalty be waived. Form 5329 will be created.
    

If you don't have a 1099-R, you can complete Form 5329 in TurboTax Desktop by going to Forms Mode. 

1. Click on Forms in the upper right hand corner of the screen, then Choose Open Form and type 5329
2. Scroll all the way down to Part IX of the form and complete the information, all the way through the Waiver section.

If you don't have a 1099-R and you are using TurboTax Online, you can't create Form 5329 using the program. Instead you will need to  Print out Form 5329 and print and mail it with your tax return, which you will need to file by mail. This method will only work if you are requesting a waiver of the entire penalty, because the penalty can't be added to TurboTax Online without another 1099-R.