Since these symptoms have been going on for quite a while, I definitely recommend that you get some medical help for dealing with them. You could start by going to see your primary care doctor
, who can perform an initial examination and help figure out what is going on.
I do thing that your suspicion that these symptoms might be related to allergy is quite likely. It turns out that allergies to indoor allergens, things like mold and mites, are very common. Classically, symptoms from allergies to indoor allergens are worse at night. This is because both mold and mites tend to be concentrated in the bedroom (mold in bedroom carpet, mites in the mattress itself); therefore, when you lay down, you are potentially exposing yourself to the highest concentration of these allergens that you have encountered all day!
Your doctor will be able to examine your eyes and confirm whether or not these symptoms are due to allergies. If so, there turn out to be a number of excellent medications that can be used to control the symptoms. These include the standard anti histamine medications that you are probably familiar with already, but also a number of different types of anti allergy eye drops.