I guess it depends on your budget (as stated above) and the year of mustang you are going to purchase.
If you have the 79-93 body, a 5.0 is a simple install. However to install a 4.6 into that same body style you will need to change the front K-member.
If you have a 94-95 stang you will also have to change the k-member if you plan on running a 4.6 as these models still had the 5.0 engine.
Obviously the 96 and newer stangs come with the 4.6, but to install a 5.0 I believe you would need to change the k-member also.
A 5.0 has some great benefits....you can purchase a cheap (low cost) stroker kit in either the 331 or 347 configuration and have an honest 300-350 rwhp natually aspirated (with a good set of aftermarket cylinder heads and appropriate camshaft).
I used to have a 347 in my 89LX coupe that was based on:
Ford Performance Solutions 347 stroker kit with cast crank, H-beam rods, J+E flat top pistons, Edelbrock Performer RPM heads, X-camshaft, and a cobra upper/lower intake. It made 312 rwhp and 378 lbs. of torque naturally aspirated. It got 19 miles to the gallon with 3:73 gears and a T-5 transmission. On a small shot of nitrous (73-nos jet) I made 425 rwhp and 530 lbs. of torque. It ran a best of 10.78 @ 125mph in the quarter mile with a weight of 3210 pounds and did it all on 93 octane pump gas.
A 4.6 will be more of a challenge to have that kind of natual rwhp.
The 5.0 has some proven technology behind it and pick up any car magazine and you can base your combination on 1,000's that other people have run and have a good idea about what your car will run (at dragstrip) and how it will perform as a daily driver.
The 4.6 is now coming into its own and it is definitely the way of the future. However you may find that it is more expensive compared to the 5.0.
By the way, I currently own a 1988 Gt and a 1998 Gt. The 1988 Gt has GREAT low end torque.....something that my 1998 Gt seems to be missing.
To each his own, good luck with whatever you choose.
That's my 2 cents anyway...keep the change!
I've put so much time, money, and effort into the mod motor I'd have to say 4v or 2v mod motor first. However, there are so many badass aftermarket high performance parts for the push rod stuff it would a lot of fun, and maybe cheaper to build a 302 or 351 based motor. You have so many choices of great heads, intakes, power adders, its hard to ignore.
Handle more power with a 5.0 I doubt that. 4 bolt main and cross bolts I think you have a much better chance of holding a crank in the block on a Mod motor. With quality forged internals your Mod can out power and out last a 5.0. As time passes you are seeing Mods going faster and faster and guess what, all on a basic ford block, no one else makes them because there is no need to at this point. There are new Mod parts coming available all the time, as more people buy them in time they get cheaper. Parts for Fords 302/5.0 used to be very expensive also. Now they are as cheap as Chev parts.
460 Big Block with dual stages of Nitrous. But hey, that's just me. I would go with the 5.0 stroked and built, much cheaper and can handle more.