I really like Cryptoport but only disadvantage is you need to put manually the unit prices for transactions.
How would a Portfolio Manager app that is not the exchange upon which you made the transaction be able to track the exact price you paid without you entering it manually? You're seeking a Portfolio Manager app that is fully integrated with all the exchanges you work with. This would be great, but this industry is way too young to have such integration.
What other features are you looking for?
If this is the only issue, find an exchange that can hold most of the coins you want, use that as your primary exchange (and therefore portfolio manager) and pray that they don't steal your coins!