There must be thousands of alternator manufacturers out there. For a commercial venture quantity and reduction in price will no doubt be the main influence.
Hydro is generally easier than wind, the conditions are much less variable and absolute efficiency at low output is less important. You will probably end up with an iron cored pma with neo magnets. The air gap machine may compete but you are not so worried about low load losses. The iron cored machine will probably have a good enough efficiency over the range you want if you choose it right.
The only advice I can offer is forget single phase, any multiphase machine will do, but again it is unlikely that you need to consider other than 3 phase.
You will be rectifying to dc so the number of phases has little effect. It is unlikely that you will see much benefit from other than simple diode rectifiers unless you choose an odd machine design with high leakage reactance.
I would strongly suggest that you aim for a voltage that will get you charging 48v in the worst water conditions. You are not afraid of technology and you will simplify the turbine requirements immensely if you use some form of buck converter to match the turbine to the battery load. You could incorporate mppt if you want it to adapt to water conditions automatically. Basically I am suggesting you choose your alternator to cover the lowest output case and use something similar to a MX60 to match your load. You may need to look at a higher voltage device if you want to cover all cases with a single alternator or you can have several alternators to cover your range.
Don't be tempted to cover a voltage range by using star/ delta, the delta option is not good with rectifier loads. Series parallel winding connection would be more practical.
If you go for small quantity production you will likely be forced to use standard motor punchings. These are not ideal for low speed PMAs but will work.
The number of poles doesn't matter a lot, but generally the lower the speed the larger the diameter and the higher the pole number for best economy. Motor cores are intended for high speed and small pole numbers, you can increase pole numbers but you end up with deep slots that may not be to your advantage.
Stacks of big vehicle alternator punchings may be a good starting point as cost may be more of a factor than the fact that they use the cheapest core materials.
Flux