In the Voyager episode "Relativity", the events are centered partially around the timeship of that name. But if you are exploring (or monitoring) time rather than space, what is the reason for doing so from a ship off in space somewhere rather than a surface base on a planet or appropriate moon (or possibly even an orbiting space station), which would surely have easier access to most resources and avoid many of the problems which, even in the Star Trek universe, exist in space travel?
You would create a "timeship" for the same reasons you create a spaceship, to go places and in this case into times, that have localized temporal anomalies that need investigating. The Wells-class timeship, Relativity, still has all of the responsibilities of a ship of the Federation of the 29th century, with the additional duties of investigating temporal anomalies which they appear to be able to be detected before their effects can be felt in the timestream.
In the Voyager episode "Relativity", the placement of a bomb hidden in the timestream makes it necessary for an agent to be able to be placed both in space and in time. The image below shows a display from on board the Relativity as the crew attempts to rescue Seven of Nine from a point in the timestream.
Although it's not part of the Trek canon, this precise issue was dealt with in the Red Dwarf episode "Out of Time" where the crew use their new-found time machine to travel to the 1400s. It then become apparent that without an FTL drive, they're precisely where they started, just farther back in time.
Rimmer: So ... forgive me if I'm being thicker than the offspring of a village idiot and a TV weathergirl, but what exactly was the point of that little exercise? Fun though it was drinking in the heady medieval atmosphere of pre-Renaissance deep space, the drive is next to useless, yes?
Kryten: Well, at the moment, yes, but should we ever acquire a faster-than-light drive, we will have the combination to travel anywhere and anywhen.
I would suggest that a ship is vital if you wish to travel in time.
There's one thing that everybody conveniently leaves out of time-travel films: things move.
Back to the Future is especially guilty of this.
Stand in one spot. Now travel five minutes into the past. Now, as you asphyxiate in the vacuum of space, look around. See that? That's the Earth, and it's coming your way.
Time travelling must necessarily involve movement relative to something. If you want to travel in time to Earth in the 1400's (for example), you don't just need to jump through time - you also need to jump several billion kilometres through space to where the Earth was at that time.
So a ship is the ideal vessel for that.