I would get contractor estimates so you have some more concrete numbers.

An area known as "up and coming" with a handful of craft breweries and  neat restaurants within a block. 

Hey @Pete Mathias, you’re probably looking at a low C Class area but it varies quite a bit block by block so it’s tough to say with 100% certainty. 

Unlike poured foundations or brick/cement-block foundations, the stones aren't very uniform, so there is a little art to replacing individual stones.Sometimes you have to repoint the mortar in between the stones.

Another option might be Concrete. 

Pouring concrete or doing exterior stucco isn't impossible, but the right people have to handle the work.

Main problem is, there is what looks like 1-2 feet of still dark water sitting in the basement ( completely concrete unfinished basement no drywall or flooring).

I've had substantially renovated properties (kitchens, baths, wiring etc.) appraised over a 1% RV when the one 2-3 blocks over (or on the same block) was under 1% RV.Happy hunting!

We've had two completely different ARV appraisals on basically the same home within 2 blocks.   

Bought for around $700K 4/5 years ago a few blocks outside of Union Square.