These are always a bit tricky.

Federal worksheet check the box to e file NY and NY 204-LL

Form 204 LL line 4 or 6 whichever one applies, click on that and fill out the worksheet.  Make sure you get the checkboxes 1-3 above.

Click EFILE payment form ready to e file

Let me know if that doesn't work

It was important to indicate in one of the three questions that the LLC in question had income from NYS sources.  Although revenues were zero, if you advise that you don't have NY Source income there is no liability for this tax. My client preferred to pay the $25 tax and remain in good standing.   

Make sure that right return type is checked in information worksheet. for by default it checks Partnership return, instead of LLC.