Temperature Controlled LED
It's running in an indoor environment, and I would expect it to be in
  the range of 15-30°C. It would be a few different channels with one
  LED, LED Vf ~2.1V, up to 100mW, probably something similar to EPITEX
  L625-36


The best way to keep LEDs running cool is to use an LED with high efficacy and a thermal pad.  

The Epitex L625-36 @ 50 mA, 2.2V Vf = 110 mW, outputs 23 mW of light.  Efficacy = 23/110= 20.9% 

The problem is cooling an LED embedded in 3 mm of epoxy resin with no thermal pad. 

Now if you were to use a Cree XP-E P/N XPEBRD-L1-0000-00901
It has a photon output of 2.10 µmol/s (400 mW Radiant Power) @ 350 mA x 2.2V  Vf = 770 mW total power dissipation.  Efficacy = 400/770 = 52%.

52/20.9 = 249% so you will have ~2.5x less heat to deal with due to efficacy. 

Plus the total power dissipation will be lower due to a ~10% lower  Vf at lower current. 

Less heat flux makes thermal management easier.  

15°C variation in ambient is the issue.  If ambient were kept constant there would be no LED junction temperature deviation once the system reaches thermal equilibrium.  Red LEDs are more susceptible to variation in temperature that all other colors except amber. 

Temperature vs. Irradiance

Rather than thermal management you may want to consider using a photo diode rather than thermistor to keep the irradiance constant rather than temperature. 

The circuit below (yellow) will regulate LED temperature but does so by changing the current which affects irradiance. But if you replace the thermistor with a photo diode it will keep the irradiation constant. 

This circuit incorporated with a linear constant current regulator would keep it very simple with very little ripple current.