CB -
I'd be inclined to use the GL-3 if that's what the manufacturer recommends. My guess is that the GL-5 rating was probably in existence when the golf cart was built, and that it wasn't specified for a reason.
As the following text from a John Deere forum points out, GL ratings are different from API oil ratings in that higher ratings don't mean better performance for a given application. One example of this is the use of a GL-5 gear oil in a component that contains "yellow metals" - brass, bronze, copper etc. Higher GL ratings tend to have higher sulphur content which can be murder on these metals (some of which are often found on synchronizers). Maybe your golf cart components contain such metals.
Sometimes you don't want any EP (Extreme Pressure) additives at all, so a GL-1 might be specified. Or sometimes you find out, as I just did, that you're better off not using gear oil at all for certain applications. In my International Loadstar 5-spd synchro transmissions, I'm switching from 80W-90 GL-5 gear oil to straight 50-weight motor oil, and am told that my synchros will love me for it. (My I-H websites confirm this - who knew?).
Here's the text from that JD website - interesting reading.
<font color="blue"> Gear Oil Ratings
API Gear Oil Service Classifications
<font color="red">The API System designates gear lubricants by the types of service for which they may be suitable. This is not a rating of performance. </font>
API GL-1
For service in automotive-typed spiral bevel, worm gear axles, and some standard transmissions, operating under conditions of low pressures and sliding velocities. Rust and oxidations inhibitors, foam suppressors, and pour point depressants may be used, but friction reducers and extreme pressure agents must not be used.
API GL-2
For automotive-type worm gear axle service, under conditions of load, temperature, and sliding velocities where gear oils for Service GL-1 are not adequate.
API GL-3
For service in manual transmissions and spiral-bevel gear axles, under moderate conditions of speed and load. The service conditions are more severe than those of API GL-1 services, but not as demanding as for GL-4.
API GL-4
GL-4 is used for manual transmissions spiral-bevel and hypoid gears in moderate service.
API GL-5
This is the preferred oil in John Deere compartments when gear oils are recommended. API GL-5 is for service similar to GL-4 but for more severe conditions. It applies to conditions encountered in hypoid gears and other equipment operated under high speed, shock load, high speed, low torque; and low speed, high torque conditions.
API GL-6
API GL-6 is an obsolete classification
</font>
Hope this helps - again, I'd go with the GL-3 and not look back.
John