Since you mention a charging port, may I assume you are referring to a Micro USB? If so I would be really leery of using anything that you may not be able to fully remove.

A waterproof box would be the best bet. REI may have exactly what you need. At least worth a try, REI used to carry a lot of waterproof containers for cameras, phones and the like for white water rafting, diving etc.

If a box is simply not an option and the area around the USB opening is completely smooth, that is no seams that would be hard to seal, I would recommend duct tape or some other waterproof/resistant tap.

Also, if you can plug the opening with a piece of cardboard or a small piece of tape to prevent glue from entering, a blob of hot melt glue on the surface is also an option, I have seen variants that are intended to be removed. It has the benefit that it is solid and tack free when it cools down, while mounting putty remains soft and sticky - it will stick to anything that comes in contact such as fabric and may pull off if the stick is better to the contacting surface allowing water to enter.