While probably not what you meant, strictly speaking "The Big Bang" takes place at the end of the universe; it just so happens that the universe is tiny, so that's not the feat it used to be:
Doctor: Rory! Listen, she's not dead. Well, she is dead, but it's not the end of the world. Well, it is the end of the world. Actually, it's the end of the universe.
Doctor Who Series 5 Episode 13: "The Big Bang"
There's possibly one other time, but it's never been explicitly confirmed. In "Hell Bent", the Doctor travels to the End of the Universe1 to shake off the Time Lords; he implies it's the only way he can2:
Doctor: Now we just have to shake off the Time Lords. There's only one place we can do that.
Doctor Who Series 9 Episode 12: "Hell Bent"
There's one other time in the show where he needs to escape the Time Lords, and that's at the very end of the Second Doctor's run, when he's contacted the Time Lords for help and then runs away to avoid being put on trial for "meddling." He attempts to take the TARDIS somewhere he (and his companions) will be safe from them:
Zoe: Doctor, what on Earth are you doing?
Doctor: I'm trying to make a quick transference jump. We've got to get away from here to somewhere safe. Ah, we're landing.
Doctor Who Season 6 Episode 7: "The War Games"
Of course, this doesn't exactly mesh with the concept of the end of the universe as shown in more recent episodes, for two reasons:
- The TARDIS scanner shows lifeforms (alligators) outside of wherever they are
- The Time Lords catch them anyway
So either he didn't actually go to the end of the universe here, or he tried and just didn't go far enough.
In any case, those (the above and the examples from the question) are the only times we can confirm having seen the Doctor visit the end of the universe on television3, but it's not the only time he's been:
In "Forest of the Dead", River mentions that she and the Doctor visited the end of the universe together:
Anita: You say he's your friend, but he doesn't even know who you are.
River: Listen, all you need to know is this. I'd trust that man to the end of the universe. And actually, we've been.
Doctor Who Series 4 Episode 10: "Forest of the Dead"
Whether or not she's referring to the events of "The Big Bang" is unclear; it's certainly a possibility
Once again based on the Doctor's assertion that the end of the universe is the only place to shake a Time Lord tail2, it's possible he went there on his very first escape from Gallifrey (before the show even started), but obviously we have no confirmation of this
While not remotely what the question is actually asking, there have been several occasions where the Doctor goes to the spatial end of the universe, and passes beyond it. One of these is in "The Doctor's Wife":
Rory: But what is this place? The scrap yard at the end of the universe?
Doctor: Not end of, outside of.
Doctor Who Series 6 Episode 3: "The Doctor's Wife"
Another is "Full Circle", a Fourth Doctor story where he and Romana travel to "E-Space", where spatial coordinates are negative (i.e. beyond zero):
Romana: Negative coordinates.
Doctor: Yes that settles it. We're out of our own time and space, Romana.
Doctor Who Season 18 Episode 3: "Full Circle"
Three stories take place in E-Space ("Full Circle", "State of Decay", and "Warrior's Gate"), before the Doctor returns to normal space.
The final Fourth Doctor story, "Logopolis", revealed that in a manner of speaking most of the show has taken place after the end of the universe; it was supposed to end some time before, but the Logopolitans have been skirting the second law of themodynamics, keeping the universe from ending:
Monitor: Yes, Doctor, you were right. Our numbers were holding the fabric of the universe together.
Nyssa: But how? Surely in a closed system like the universe, entropy is bound to increase?
Monitor: Certainly. The universe long ago passed the point of total collapse.
Doctor: Passed the point?
Monitor: If it had remained closed. But we have the means to postpone the time.
Doctor Who Season 18 Episode 7: "Logopolis"
1 Not to find the Restaurant, sadly
2 It's worth noting, as Mike Edenfield does in comments, that this is only one possible interpretation of this line; another one is that the Doctor had to go that far not so the Time Lords couldn't find him, but so they couldn't find Clara. If that's the interpretation you favour, you can disregard this example
3 There are perhaps more occurrences in the novels or the Big Finish audios, but I don't know anything about those so I'm not going to care