Two big biotechs have been big busts for investors so far in 2017. Shares of Biogen (NASDAQ:BIIB) and Gilead Sciences (NASDAQ:GILD) are both down year to date, with Gilead's shareholders experiencing the worse pain.

Should long-term investors consider either one of these biotech stocks? If so, which one is the better choice? Here are the cases for Biogen and Gilead Sciences.

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The case for Biogen

Perhaps the best immediate case for buying Biogen stock is the tremendous potential for Spinraza. The U.S. Food and Drug Administration approved the drug as a treatment for spinal muscular atrophy in December. Although it's still early in the launch for Spinraza, analysts think the drug can achieve peak annual sales of around $2.5 billion. Biogen must pay Ionis Pharmaceuticals royalties on all sales of Spinraza, but it should still make substantial revenue from the drug.

While Spinraza picks up momentum, Biogen is still getting solid production from its multiple sclerosis (MS) franchise. Sales for Tecfidera and Tysabri continue to grow, albeit slowly. Still, though, increased sales for the two MS drugs plus Zinbryta has been enough to more than offset declining sales for Avonex, Plegridy, and Fampyria. 

Biogen is also seeing strong sales for Benepali, its biosimilar to autoimmune disease drug Enbrel. The biosimilar was approved in Europe early last year.

Buying Biogen stock also gives investors a lottery ticket of sorts with the biotech's late-stage pipeline. Biogen has two experimental Alzheimer's disease treatments in phase 3 testing -- aducanumab and E2609. Aducanumab is especially interesting, because the drug showed promise in a phase 1 study of slowing down progression of Alzheimer's disease. 

The case for Gilead Sciences

The best thing going for Gilead Sciences right now is what made the biotech successful early on: its HIV franchise. Genvoya has been a huge success. Sales for Descovey and Odefsey are rapidly growing. Although much of the growth of these three drugs has been at the expense of existing products Truvada and Atripla, Gilead is still experiencing overall growth from its HIV lineup.

Gilead's greatest challenge, though, is with its hepatitis C drugs. While sales continue to grow for Epclusa, it's not nearly enough to make up the continued revenue nosedive for Harvoni and Sovaldi. The biotech's hep C franchise should get a small boost if the sofosbuvir/velpatasvir/voxilaprevir combo treatment wins approval later this year. However, probably the best Gilead can hope for is stabilization of hep C drug sales sometime in the future.

Sales for Gilead's HIV franchise, on the other hand, could kick into higher gear if the company's bictegravir/F/TAF combo gains regulatory approval. Gilead recently announced that the combo met primary endpoints in four late-stage clinical studies. The biotech plans to submit for U.S. regulatory approval in the second quarter of this year and for European approval in the third quarter.

There's also a lot to like with Gilead's pipeline. The biotech's ASK-1 inhibitor selonsertib has showed promise in treating non-alcoholic steatohepatitis (NASH) and is now in a late-stage study. Gilead has high hopes for winning in the potentially lucrative NASH market, with two other mid-stage candidates targeting the indication. The company also intends to stake its claim in the autoimmune disease market if all goes well in late-stage studies evaluating filgotinib in treating rheumatoid arthritis, Crohn's disease, and ulcerative colitis.

One other thing that investors will find attractive about Gilead Sciences is its dividend. Gilead stands out as one of the top biotech dividend stocks, with a current yield of 3.21%.

Better buy

Both Biogen and Gilead Sciences face plenty of unknowns. Biogen's MS franchise could have stiff competition soon. There is plenty of doubt as to whether its pipeline candidates for treating Alzheimer's disease will prove to be successful. Gilead doesn't know when the bleeding will stop for its hep C drugs. The big biotech also faces competition in HIV and risks with its pipeline.

Even with all of this uncertainty, though, I think Gilead is the better buy. It comes down to simple math. Gilead had free cash flow of $13.82 billion over the last 12 months. You can buy that cash flow for less than nine times estimated earnings. Biogen had free cash flow of $1.7 billion during the last 12 months. Its stock trades for 11 times estimated earnings.

Granted, Gilead's cash flow is slipping as sales for Harvoni and Sovaldi decline. However, it will take a long time before Gilead generates less cash flow than Biogen -- if ever. What the company will do with the cash that it spins off (specifically, paying increasingly higher dividends and making acquisitions) is the reason why, in my view, Gilead tops Biogen.

This article represents the opinion of the writer, who may disagree with the “official” recommendation position of a Motley Fool premium advisory service. We’re motley! Questioning an investing thesis -- even one of our own -- helps us all think critically about investing and make decisions that help us become smarter, happier, and richer.