tl;dr: Park your ISS-like space station above 700 km and there is a good chance it will only lose 100 m/s in 1,000 years due to atmospheric drag at least (and 2000 km for a million years). However, there are other problems
This is a really interesting question! Just for example, the LAGEOS satellites are about 6,000 km above the Earth's surface and are expected to re-enter the atmosphere in 8 million years or so. But they are spherical and dense, whereas a space station may be non-aerodynamically shaped and have a low density.
Let's look at the current TLE for the ISS from https://celestrak.org/NORAD/elements/stations.txt
ISS (ZARYA)
1 25544U 98067A 19203.81086311 .00000606 00000-0 18099-4 0 9996
2 25544 51.6423 184.5274 0006740 168.1171 264.4057 15.50995519180787
The value for B-star is see this 18099-4
which is 0.18099E-04 which is 1.8099e-05 which is pretty big, as it should be for a hollow space station with big solar panels. It has units of inverse Earth radii (see this from this).
Wikipedia's BSTAR gives the following equation for acceleration due to drag:
$$a_D = \frac{\rho}{\rho_0} B^* v^2$$
where $\rho_0$ is a reference density and is about 0.1570 kg/m^2/Earth radii and $v$ is velocity presumably in m/s.
Calculating time to reentry requires some calculus, so let's just estimate the time it takes to lose 100 m/s in velocity.
$$\Delta t = \frac{\Delta v}{\frac{dv}{dt}} = \frac{\Delta v}{a_D} $$
If we then set $\Delta t$ to 1000 years or $\sim 1000 \times \pi \times 10^7$ seconds, we get $a_D \sim 3E-09$ m/s^2 for that 100 m/s loss.
Putting that back into the first equation and using the ISS' $B^*$, we get
$$\rho = \frac{a_D \rho_0}{B^* v^2} $$
The funky units (Earth radii-based) work out and the atmospheric density is about 8E-13 kg/m^2 based on an orbital velocity of about 7000 m/s
What altitude is that? It depends greatly on the Sun's activity. The plot below puts it as low as 380 km during a solar minimum, but up at 700 km during an active Sun.
This link found in this answer puts 8E-13 kg/m^3 closer to 600 km for an active Sun.
That link shows 8E-16 (for 1 million years) at about 2,000 km.
So park your ISS-like space station above 700 km and there is a good chance it will only lose 100 m/s in 1,000 years due to atmospheric drag at least, and above 2,000 km for 1,000,000 years. However, there are other problems due to a big patch of space junk in the 600 to 1000 km neighborhood.
Found in this answer, from https://en.wikipedia.org/wiki/Scale_height Wertz et al. SSC12-IV-6, 26th Annual AIAA/USU Conference on Small Satellites.
