I vacationed to Cebu last year and had the chance to visit all three shops in order to scrutinize the ukes.
In order of quality, Ferangeli is definitely the best of the three. Nakakatuwa, they have a PRS style doublecut uke, and the mango wood ukes have awesome looking grain. They are also very good with their pearl inlays. Better email/call them in advance to ask about what they have in inventory, and ask them to send pictures. Madalas kasi, they take their good ones on displays/conventions.
I'd consider Susing's middle to low quality. What I like about them is that do a lot of novelty guitars and ukes, ranging from Selmer style guitars (Django Reinhardt) to cigar box ukes. As with Farengeli, call them in advance if you want to look at a particular novelty guitar.
Alegre, I'm sorry, but I consider them low quality. A painted fretbaord is a deal breaker for me.