An IR thermometer is not likely going to give you an accurate temperature reading. There will likely be a large temperature gradient from the die to the case.
I would highly recommend reading up on emissivity of materials. Here's and experiment to try: Put a piece of black electrical tape on a shiny metal object and allow it to come to the same temperature of the object. Take a temperature reading on both surfaces and compare. Please share you results.
As far as a temp for the LDs, you would have to check on the specific data sheet.
I think you missed the point. The temperature will be higher at the actual laser die than the surrounding areas. You can take your IR thermometer and measure the temperature of the case, but how would you measure the temperature of the die? Having said that, the more cooling the better. For longest duty cycles build a TEC.