Ok, I figured out a work around for this if anyone's interested. Substitute NY for your state.
First, enable Table shipping. Go into the php file and change "Table" "Best Way" to whatever you need, like "Store Pickup" "Local Sales Tax Apply".
Set the numbers to 25:0,50:0,10000:your local sales tax%
For Queens county, which is 8.375% tax, I made it 25:0,50:0,10000:8.375%
Don't forget the percent sign...this will add whatever percent your local sales tax is to the order total.
Tax class - none.
Create a separate tax zone with a rate of 0% called NY - Local Pickup. Add a statement to the Table file so that people with your state as their shipping address know to change their state to NY - Local Pickup before selecting local pickup, so that they are not charged twice for the local tax. People with out of state shipping addresses won't need to change anything. For this I said "Store Pickup - If your SHIPPING state is NY, you must change it to "NY - Local Pickup"
Works well. Screen shot: