If you have carpet and can afford it, see if you can hire a professional carpet cleaner that knows how to deal with pet odors and allergens and look for mold and mildew.
Biggest sources of indoor allergens are carpets that are harboring pet odors, mold, and mildew.
Next is the furnace as I already mentioned.
After that its is dust and curtains. People forget to clean their blinds and curtains and then when they open the window all the dust is blown everywhere.
Ceiling fan dust as well.
Always wipe everything down with a damp cloth when dusting or sweeping.
Dust will float around for a day, otherwise.
Hope you feel better soon.
Oh, another thing that helped my husband was having him use a pillow for allergy suffers, and having him wipe his own hair and face with a damp cloth before going to bed.
Your hair will also pick up a lot of crap of the day and then you rub it all over you clean pillow and breathe in all that crap all night long.