It is interesting that your MD offered to perscribe you Omacor (the perscription fish oil) because it is approved by the FDA for the treatment of high triglycerides. Flameout seems to be an extremely purified product right up there with Dr. Sears' OmegaRx fish oil. If I remember correctly the EPA/DHA per serving between Omacor is similar to that of Flameout.
In regards to raising your HDL I would say exercise is your best bet. As men we are doomed to lower HDL levels (compared to women) but exercise can compensate for the difference and get your level where they need to be.
Personally I would skip the Omacor and go with Flameout. I know some people are still recommending the Kirkland brand but the toxins in fish oil are so nasty why take the risk of a lower quality product. I know that Consumer Reports gave them a favorable review but that was several years ago and you will need to take a much higher dosage than 1 serving of the Kirkland brand.