By "shoreline" I assume you mean "shortline." Without knowing which railroads they are, I really can't say anything specific. In my experience, some (but certainly not all)tourist lines are real shoestring operations, run by people whose dreams of profit-making are not well-founded. There are some who are for-profit businesses who actually depend to some degree on volunteer labor (there are some people who are so enamored of being around steam that they will settle for very low wages or work for free--it's one thing to volunteer at a non-profit museum, another to make money for someone else and not get paid for it). Some are a house of cards like the whole Iowa Pacific thing. Another thing to consider is that tourist railroads essentially sell leisure-time entertainment, one of the first things people cut back on if the economy tanks and they have financial constraints.

A freight-hauling shortline may also be run by management with a poor grasp of the reality of their profit-making prospects (like any business), although there are many that are well-run. I wonder what makes the one you refer to "less than great." Shortlines whose traffic base depends on one or two customers may be in big trouble if those customers go out of business or relocate. If it's a matter of pay vs. working conditions, you just have to compare it with other jobs you might be able to get. And of course, getting hired by a Class I mainline railroad is no guarantee of full or sustained employment either. The short answer is find out all you can about each railroad's economic prospects and working conditions, then make your best informed guess.