Pt100 tends to need 4 wire connection, while PT1000 might still get away with 2 wires.
With the expensive wire based resistors PT100 tends to be slightly more accurate. With thin film sensors the problem is more with the contacts and thus with slight favor for PT1000. The other advantage of PT1000 is less sensitivity to thermal EMF - the advantage of less aging at high temperatures is with PT100, but not relevant here. Also cable insulation is easier with PT100 - but this is more like a high temperature problem too.
Self heating and noise are the same, if the same power is used - these two are points one can choose the balance.
Both types work, I would slightly prefer PT1000. However there might be better offers on precision PT100s. I would look for ready made probes, not just a bare sensor.