Isopropanol in contact lens solution plastic bottle I have a rather large plastic bottle of isopropanol ($99.7\%$), and I wanted to store some of it in a smaller, more handy container. I have two empty plastic bottles from contact lens solution that I wanted to use, but I'm not sure if it is safe for storing them in there for longer periods of time.

One of them has a 01 symbol inside a triangle, from which I concluded that this means PET and it also has a number 3 inside a circle (I'm not sure what that means).

The other one is HDPE (2 in a triangle) and has a number 5 elsewhere. Are both of those safe for long term storage of isopropanol?

I do intend to mark them very clearly.
Based on your description, it looks like you've determined both plastics correctly. In general, they both would work fine for storing isopropanol; however, according to the Thermo Fisher's Labware Chemical Resistance Table, HDPE is preferred: 

$\ce{i-PrOH}$ – PET


$\pu{20 ^\circ C}$: E Little or no damage after 30 days of constant exposure;  
$\pu{50 ^\circ C}$: N Immediate damage may occur. Not recommended for continuous use.


$\ce{i-PrOH}$ – HDPE


$\pu{20 ^\circ C}$: E Little or no damage after 30 days of constant exposure;  
$\pu{50 ^\circ C}$: E Little or no damage after 30 days of constant exposure.