I have an LLC which is taxed as an s-corp. I live in DC but my LLC and s-corp are in Virginia. VA and DC have reciprocity. as the only shareholder who do i pay tax to?

Did the S-Corp issue you a W2 as well?  

OP is the only shareholder, so hopefully, YES.

Yes i will be paying myself a salary, and i know that the salary portion will by taxed by DC not VA per the reciprocity agreement.  The question I have is what about the pass-through income/profits? This is not salary, and wouldn't be considered earned by an employee, I see i need to make estimated tax payments but I can't find a clear cut answer as to whom DC or VA.

I'm not familiar enough with states with reciprocity, I live in the west coast, we don't have much of that out here.

I would "guess" the pass-thru profits would be taxed in your resident state.

I highly recommend you seek local assistance with these questions ... a practitioner in your area would be well versed in the reciprocal situation.

I have not delved into this in depth, however, the following are my comments:

• It would be a good idea to have a meeting with a local tax professional to get started down the right path. 
• Reciprocal agreements between states, when they exist, pertain to wages earned, nothing more.  These agreements make sense for those that live in one state and commute to work in another state.  Not all states enter into agreements in these cases, but Virginia and DC do have reciprocity. 
• As noted above, the reciprocal agreement between Virginia and DC is ONLY for wages earned; income reported on a W-2 and applicable withholding.  So in your case, all your W-2 wages would have DC tax withheld not Virginia.
• You will report your S corporation income that is earned in Virginia on a Virginia Form 502.  At the end, I have included a link to some general commentary on this matter.
• It appears that Virginia allows for the filing of a composite tax return for nonresidents, however, the discussion in the link below indicates "...two or more nonresidents..." You indicate that you are the sole shareholder so you would not be eligible to file a composite tax return.
• Since you are not able to file a Virginia composite tax return, you will need to file a Virginia nonresident individual tax return and report your Virginia sourced income from the S corporation.  Do not report your W-2 wages on this Virginia nonresident income tax return.
• When you file your DC income tax return, form D-40, you will also need to complete schedule U.  This is where you will receive credit for taxes paid to Virginia related to the S corporation earnings.  You receive this credit since you will also report the S corporation earnings on your DC return and this minimizes any double tax impact.  It is not always a $ for $ credit, but it does minimize the impact of paying tax on the S earnings twice.
• You will also need to review the Virginia requirements related to whether or not the S corporation is required to remit withholding on nonresident S shareholders.  Any withholding remitted by the S corporation on behalf of a nonresident shareholder will then be reflected on the Virginia nonresident income tax return when filed.
• So as you can see, there are many pieces involved here and getting started correctly is critical; which means consulting with a tax professional.