It depends on the circuit of your amp. Both rectifiers have the same pin out and are full wave, but operating parameters are different. For instance, the 5AR4 has a plate resistance of around 80 ohms, while the 5Y3 has resistance of 400-450 ohms I believe. So if you have a fairly high current amp, the 5Y3 will have a much greater drop in voltage during loud passages, thereby a reduction in power. The amp may not sound as good as distortion will increase. You should contact the manufacturer to determine if the circuit allows for that.
