In order from lowest to highest cost (roughly):
1) For something simple like this, grease filled wire nuts aren't the most beautiful option, but you can readily pick up a pack of them for a few bucks at your local hardware store.
Pros: Cheap, available, work
Cons: Messy if you need to disassemble, clunky, look bad
2) You could also use grease-filled IDC (insulation displacement) connectors.
Pros: Cheap, available
Cons: Like other IDC connectors, not great at high current, messy to service
3) Use adhesive-lined heatshrink tubing. It works just like heatshrink, but has an inner liner of hot melt glue which will melt as the tube shrinks, creating a (mostly) environmentally protected connection.
Pros: Moderately easy to service, fun to shrink, looks clean
Cons: More expensive, is stiff when finished (can cause stress risers in the wire)
4) Use adhesive-lined crimp splices or adhesive-lined solder splices. Outer sleeve is similar to adhesive-lined heashrink but is usually transparent for inspection. Crimp style are crimped, then shrunk. Solder style have low temp solder pre-applied inside, just insert the wire, apply heat, and you've got a waterproof solder splice.
Pros: Professional, adhesive layer can be inspected to ensure full coverage
Cons: Really, really expensive.
Ask you FR4 supplier about conformal coating options. They can mask it off, on the windows of the LED's and such. Check the water resistance of the LED's and such exposed parts. Most electronics are, as they are washed. Conformal Coating is very common on military and automotive electronics. A long time ago, I used it on video equipment that went in the trunk of vehicles to protect from salt build up from DEW point condensation.
Best Answer
There are a variety of common materials that are available to be used as enclosures or windows for an enclosure i.e. Calcium Fluoride (CaF2, Fused Silica (FS),Germanium (Ge),Magnesium Fluoride (MgF2), Sapphire, Silicon (Si),Sodium Chloride (NaCl) to name a few. There are also IR transparent plastics. I had a similar application years ago and I started down the same path as you have, but when I started to go through all of the time in engineering and research I went with a commercially available IR camera with an IP66 rating.
If yours is a labour of learning, then Google "IR transparent materials" and in turn use them as a "window" to your enclosure for your selected sensor it would be the best place to start.
I looked very quickly on the spec sheet for your chip and I didn't notice what wavelength of IR it is the most sensitive to. You would have to ensure the "window" material is efficient in that range.