Both of them completely neutral, entirely divorced from Good or Evil. If they had any association with alignment, they would be part of the upper planes, not the inner/elemental ones.
It's just that the vast majority of life is empowered by positive energy, thus making negative energy harmful to it, that provides the false suggestion that negative energy is wrong or evil. Not at all. It's harmful yes, but to a creature empowered by negative energy (trillochs, scaeduinar, etc) the exact opposite would in their mind be true - positive energy is harmful or possibly evil.
Positive and negative energy are as good or evil as water, or fire, or a hurricane, or anything else. Their use or abuse by someone is the -only- thing that might gain some association with good or evil. Fire isn't evil, but burning someone to cinders would be. Likewise using positive energy to heal someone isn't evil, but pumping them full of it till their soul immolates certainly is. Searing a scaeduinar's body with positive energy to direly harm it would be evil, and so would using negative energy to energy drain a child: both of them equally evil.
If you're going to use one or the other as good or evil, best be associating them with some cosmological Good or Evil, and altering the flavor of the energies and their effects to match. Because at least with core, baseline D&D through most of its history, neither + or - energy has been evil in and of itself (nor their respective energy planes).