This is a very large issue, and your question is incompletely stated. Your question can't really be answered in a concise way. My opinion is the proper way to frame this question would include detail about:
What kind of work environment do you want to live in? It is difficult though not impossible to get a position in an academic lab with a Masters degree. You will have a serious ceiling on some kinds of career progression, but the trade-offs may be worthwhile. (Note: this point is a long discussion topic).
How many years can you afford to spend on education? Remember that even life in a PhD program where you receive a stipend has an opportunity cost, since you would most likely get paid more even as a Research Assistant. The median length of a PhD is about 6 years.
How much money can you spend? Many masters programs are not paid for unless you get a research assistantship. Private programs are very expensive.
Do you know what you're getting yourself into? Many Masters programs are not that different from college. PhD programs are not like college, although it might seem that way for the first year.
What kind of position are you targeting? If the answer is "tenured professor", then your choice is a PhD, although that's just the start of the road. If the answer is "I want a staff position working in a bioinformatics core or lab in an academic institution" then you may be able to get by with a masters degree.
What kind of degree program would you consider? There are many different programs out there. Some are an appendage of the computer science department and don't contain working wet lab biologists. Some are independent. Some require you to write a thesis (which is a good thing).
I recommend browsing the forum on the Science magazine careers site as this exact question has been asked several times there.