Prospero asks Ariel what time of day it is, and Ariel replies vaguely that it is after the "mid season"—meaning, it's afternoon. Prospero doesn't think much of this as an answer, clearly; he responds by saying that it is "at least two glasses" past midday. In simple terms, he is saying that it is at least two hours after noon—it's at least two o'clock in the afternoon. Prospero will be able to discern this by looking at the position of the sun in the sky.
The reason he uses the word "glasses" rather than "hours" is that, particularly because he's been on board a ship, he will have been used to measuring time with the aid of an hourglass. An hourglass was a key instrument used by sailors to make sure a record of time could be accurately kept while moving across different timezones. It would have been the job of somebody on board the ship to manually turn the hourglass upside down when the last grain of sand ran through it. This system was used to mark out shifts on ships, for example, so that people would know when eight hours had passed and it was time for those sleeping to work and those working to sleep, and so on.