A non-offensive term to call a lunatic?

"Eccentric" might fit the bill.

When addressing him, her or it, using their name is generally deemed acceptable, perhaps appending "sir", "ma'am", "oh great one" or a list their doctorates. After all, mad scientists tend to build death rays so politeness seems wise.

When speaking about them to other people, "My friend <name>, the mad scientist" seems appropriate. Perhaps "My friend Dr. <name>".

You seem to be implying that there is something wrong with being a mad scientist. On the contrary, your friend is likely an informed, intelligent, creative and unconventional person! They simply have different interests (nucleonics, genetic mutation, robotics, world domination) than the typical person (sports, TV, movies, drinking, politics). People vary; there is no specification or one true way to be human. Though I sometimes encounter... unpleasant people who seem to believe that whatever they are used to or approve of is the only acceptable way to be human, and that they can and should reject, oppress and/or kill anyone different.

I speak as one who greatly enjoys the "Girl Genius" online comic, with many mad scientist characters. Bwah-hah-hah-hah-hah! Tremble and obey!

There's always misunderstood genius.

You can make any negative comment sound less than negative by adding "bless his heart" to the end. "He's a lunatic, bless his heart." I personally go with "odd duck" quite often.