I'm no expert but it just depends on the amp and it's components.  There is a lot of speculation on the subject.  The 5Y3 will drop more voltage than a 5U4 so you are going to have a higher B+ so you will probably have to adjust your bias resistor value.  Also, a 5U4 has a higher capacitance value so your power cathode cap should be doubled.
The most important spec to check is how much draw your PT can safely handle.  A 5U4 requires a full amp more than your standard 5Y3.

Also, consider a 5V4....similar "less sag" characteristics as a 5U4 without the extra amp of current draw.

I hope you don't have a sovtek 5Y3 in there now.   

 The Sovteks don't have the same characteristic 60 volt drop @ 125 mA DC as a typical 5Y3 so by specs they aren't a 5Y3.    Watch your B+.  Their designs are very different as well and I think Sovteks  decision to call it a 5Y3 was a "sneaky" thing to do...lol