The lowest level magic item that grants this ability is already a level 3 magic item and can only be used by Shamans, and it only lets them see invisible creatures that are adjacent to their spirit companions.
So spells and magic items are out, that leaves us with: how do we keep the Wizard from flying out and nuking?
Well, a good option has already been recommended: a storm. This creates a challenging encounter for the players on the ship. It also lets you reduce visibility using sea-spray and storm water. It also discourages flight, since i would say it warrants a skill check if the winds are high enough. Reduced visibility reduces the range at which the wizard can cast their spells in the first place, which might be enough to dissuade her, particularily if it brings her within range of the enemies archers and casters, since without a defender around, she's extremely vulnerable to ranged attacks.