The bridge is generally at the top, looking over the rest of the ship.
...Although even in Gene's writing days, you'd rarely find the skipper or the first officer up there. All the real action would be in a darkened room deep down, with display screens rather than windows, and with radios rather than binoculars.
Having the bridge at the top of the ship would not be "realistic", but it wouldn't exactly be "unrealistic", either. It would be very vaguely satisfactory in the verisimilitude sense, bringing back memories of a time when there had been realism to such a placement (an extremely narrow time window after the invention of steam but before the invention of wireless), but highly satisfactory in the "wow, I can see where they are!" sense. And in a science fiction, the level of internal realism for such a placement could be established by the writers, without constraints from the real world.