PhD Bioinformatics academic career outlook
Like many other answers I am sure you will hear, it really depends what you want to do. Either path will be fine, what it will matter more in terms of job searching (academia or industry) would be: 


You research project
Your PI
The reputation of the program you enrolled in (unfortunately)


In general, doing a PhD requires patience, dedication, and hard work. Focus more on what types of projects you want to spend 4-5 years on rather than worrying about what field degree you will walk out with in the end.