That depends on whether you like re-packing your case, or whether you are familiar with each area.
Sanur is more touristy with many restaurants, shops and accommodation to suit all budgets, plus a nice beach front promonade, but Padang Bai is more like traditional Bali, a small fishing village, gateway to the Gilis and Lombok with the ferry terminal, very small village but friendly, again with restaurants and accommodation but not many shops. The locals in PB will certainly make you feel at home, unlike Sanur where you are just another tourist.
Really, it would depend on your expectations and the level of comfort. Don't expect 5* in Padang Bai.
Padang Bai has great wall diving just 5 minutes out of the harbour and almost all dive sites are within a 45 minute boat or bus ride. Sanur is further away from the Tulamben and Amed sites.
It's good to hear that you haven't booked your room yet, think you'd have hated being stuck in Nusa Dua (very sterile). Anyway, get out and about to find the
real Bali, off the tourist trail.
Happy, safe diving