I recently stayed about a week in Philadelphia and visited or walked by a few establishments. I stopped by Wayne Edwards, an independent men's retail shop, and chatted with the owner Wayne and his assistant Franz on a recent weekend. They carry RTW business and sportswear and also do MTM (Isaia). I was curious to see their shoe selection as their website mentions John Lobb. I didn't see any Lobbs but they did have a nice selection of mostly Italian makes (Bontoni and Gravati).
Wayne Edwards is perhaps the "cooler" alternative to establishment retailer Boyd's, which is also the largest men's retailer in the city. While Boyd's carries Hugo Boss and True Religion, Edwards carries PRPS raw denim and Yohji Yamamoto.
Around the corner from Edwards is the custom shirtmaker Barton & Donaldson.
The NY Times article below makes a brief mention of Philadelphia's Fabric Row Fourth Street (between South and Catherine Streets). The article came out after I had left Philly but I did manage to visit Fifth Street, a block away. Fifth Street houses a custom tailor and shirtmaker Ernesto (unclear if the shop is MTM or bespoke).
Just down the street from Ernesto is a tailoring supply shop, Charles Zarit and a nice vinyl shop, the Philadelphia Record Exchange.