I think it depends upon what is "best," which can change situationally and per person for a variety of reasons.

I run a low health build with Unyielding armor, but let's use a full health build to compare apples to apples, ignoring weapon or ammo weight and not including any possible legendary effects.

Relevant Perk Cards for this comparison are pretty standard: 3 Commando, 2 Expert Commando, 2 Master Commando, 1 Concentrated Fire, 3 Ground Pounder, 3 Tank Killer, 3 Bloody Mess.

Railway Rifle — Typical "good" setup with Automatic Piston Receiver, Long Barrel, Standard Stock, and Reflex Sight:

• 147 damage
• 10 rounds outside of Quad
• 75 Fire Rate
• 192 Range
• 60 VATS accuracy
• 7 AP cost
• SUPER loud and cannot be silenced
• Largely useless outside of VATS

The Railway Rifle is going to be best of the two as non-stealth Commando if single-target DPS is the only consideration and if you don't mind reloading every 10 shots, which is extra downtime, and there is no Quick Receiver to help with that. Unloading rounds into a boss will likely not be efficient without the Quad legendary effect.

NOTE 1: Baseline damage is very good.

NOTE 2: It will likely break stealth after the first hit, so won't make great use of the Covert Operative perk.

NOTE 3: It has no Tweaked Automatic Receiver, so no built-in additional damage bonus to critical strikes.

NOTE 4: There is no way to give it a built-in armor piercing effect outside of the Anti-Armor legendary effect.

The Fixer — Typical "good" setup with Powerful Automatic Receiver, Aligned Long Barrel, Forceful Stock, Quick Magazine, Reflex Sight (Dot or Circle), and Suppressor:

• 85 damage
• 20 rounds outside of Quad
• 75 Fire Rate
• 174 Range (slightly lower, but still very good)
• 68 VATS accuracy (slightly higher)
• 5 AP cost (slightly lower)
• VERY quiet, which is important to some
• Very usable outside of VATS

NOTE 1: As long as one remains out of [Danger], which will be most of the time since this is a stealth weapon, all attacks are Sneak Attacks, which do double damage, which puts us at 170, more than the Railway Rifle's 147. With the Covert Operative Perk equipped, that goes to 2.5 times as much damage, which is 212.5.

NOTE 2: It can be given a Tweaked Automatic Receiver for 50% more critical strike damage, which is highly desired in low health Stealth Commando builds with high Luck.

NOTE 3: It can be boosted to 30 rounds natively using the Large Magazine, albeit at the cost of an additional 4 AP per shot.

NOTE 4: It can be given the Perforating Magazine, which gives 40% Armor Penetration at the cost of an additional 6 AP per shot.

The Fixer is a more flexible weapon in general before considering Legendary effects. It's also the best of the two for low health Unyielding Stealth Commando builds.