I know of no tool for generating a universe scale map, and frankly the scale disparities would make such a thing really awkward. For example all the solar system objects that we've closely studied are within 6 light hours of the sun, the nearest other star is ~4.5 light years (~39,500 hours) away, our Milkyway galaxy is ~105 thousand light years across, the nearest other large galaxy is Andromeda ~2.5 million light years distant. In short at any scale that gives you details about any one thing the scales to either side are impossibly small on the one hand and impossibly large on the other; look at a solar system there are no other stars on the map, look at a slice of the galaxy and you can't see any of the planets (looking at the whole galaxy you even lose a lot of the smaller stars).
Star maps of a small sector or a star cluster can be created using a random number generator, likewise planetary systems for individual star systems. I used a small sample of the data from Kepler for calibration. Presentation is best done with either an oblique view that shows the three dimensional relationship between objects along three axes or a flat map with plus and minus figures for the Z axis positions.
Larger objects like galaxies or super-clusters aren't random though they have definite structure although we don't really understand the rules that govern the formation of it so random number generators aren't useful.